Line 24: | Line 24: | ||
==Data from publications== | ==Data from publications== | ||
- | The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of July | + | The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of July 10, 2016. |
#Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | #Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | ||
Line 1,052: | Line 1,052: | ||
#Uren PJ, Bahrami-Samani E, de Araujo PR, Vogel C, Qiao M, Burns SC, Smith AD, Penalva LO, (2016) "High-throughput analyses of hnRNP H1 dissects its multi-functional aspect." <i>RNA Biol</i> <b>13</b>(4):400–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26760575 26760575]; doi: [https://dx.doi.org/10.1080/15476286.2015.1138030 10.1080/15476286.2015.1138030]; GPMDB: [http://gpmdb.org/data/keyword/26760575 32]. | #Uren PJ, Bahrami-Samani E, de Araujo PR, Vogel C, Qiao M, Burns SC, Smith AD, Penalva LO, (2016) "High-throughput analyses of hnRNP H1 dissects its multi-functional aspect." <i>RNA Biol</i> <b>13</b>(4):400–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26760575 26760575]; doi: [https://dx.doi.org/10.1080/15476286.2015.1138030 10.1080/15476286.2015.1138030]; GPMDB: [http://gpmdb.org/data/keyword/26760575 32]. | ||
#Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen IS, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S, (2016) "Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i> <b>15</b>(4):1323–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26764011 26764011]; doi: [https://dx.doi.org/10.1074/mcp.M115.057505 10.1074/mcp.M115.057505]; GPMDB: [http://gpmdb.org/data/keyword/26764011 6]. | #Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen IS, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S, (2016) "Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i> <b>15</b>(4):1323–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26764011 26764011]; doi: [https://dx.doi.org/10.1074/mcp.M115.057505 10.1074/mcp.M115.057505]; GPMDB: [http://gpmdb.org/data/keyword/26764011 6]. | ||
- | #Kümper S, Mardakheh FK, McCarthy A, Yeo M, Stamp GW, Paul A, Worboys J, Sadok A, Jørgensen C, Guichard S, Marshall CJ, (2016) "Rho-associated kinase (ROCK) function is essential for cell cycle progression, senescence and tumorigenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26765561 26765561]; doi: [https://dx.doi.org/10.7554/eLife.12203 10.7554/eLife.12203]; GPMDB: [http://gpmdb.org/data/keyword/26765561 28]. | + | #Kümper S, Mardakheh FK, McCarthy A, Yeo M, Stamp GW, Paul A, Worboys J, Sadok A, Jørgensen C, Guichard S, Marshall CJ, (2016) "Rho-associated kinase (ROCK) function is essential for cell cycle progression, senescence and tumorigenesis." <i>Elife</i> <b>5</b>:e12994; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26765561 26765561]; doi: [https://dx.doi.org/10.7554/eLife.12203 10.7554/eLife.12203]; GPMDB: [http://gpmdb.org/data/keyword/26765561 28]. |
#Ma Y, Gao J, Yin J, Gu L, Liu X, Chen S, Huang Q, Lu H, Yang Y, Zhou H, Wang Y, Peng Y, (2016) "Identification of a Novel Function of Adipocyte Plasma Membrane-Associated Protein (APMAP) in Gestational Diabetes Mellitus by Proteomic Analysis of Omental Adipose Tissue." <i>J Proteome Res</i> <b>15</b>(2):628–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26767403 26767403]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01030 10.1021/acs.jproteome.5b01030]; GPMDB: [http://gpmdb.org/data/keyword/26767403 12]. | #Ma Y, Gao J, Yin J, Gu L, Liu X, Chen S, Huang Q, Lu H, Yang Y, Zhou H, Wang Y, Peng Y, (2016) "Identification of a Novel Function of Adipocyte Plasma Membrane-Associated Protein (APMAP) in Gestational Diabetes Mellitus by Proteomic Analysis of Omental Adipose Tissue." <i>J Proteome Res</i> <b>15</b>(2):628–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26767403 26767403]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01030 10.1021/acs.jproteome.5b01030]; GPMDB: [http://gpmdb.org/data/keyword/26767403 12]. | ||
#Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM, Aebersold R, Menke FL, (2016) "Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase." <i>EMBO Rep</i> <b>17</b>(3):441–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26769563 26769563]; doi: [https://dx.doi.org/10.15252/embr.201540806 10.15252/embr.201540806]; GPMDB: [http://gpmdb.org/data/keyword/26769563 64]. | #Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM, Aebersold R, Menke FL, (2016) "Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase." <i>EMBO Rep</i> <b>17</b>(3):441–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26769563 26769563]; doi: [https://dx.doi.org/10.15252/embr.201540806 10.15252/embr.201540806]; GPMDB: [http://gpmdb.org/data/keyword/26769563 64]. | ||
Line 1,148: | Line 1,148: | ||
#Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E, (2016) "Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes." <i>Cardiovasc Res</i> <b>110</b>(3):346–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27095734 27095734]; doi: [https://dx.doi.org/10.1093/cvr/cvw081 10.1093/cvr/cvw081]; GPMDB: [http://gpmdb.org/data/keyword/27095734 12]. | #Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E, (2016) "Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes." <i>Cardiovasc Res</i> <b>110</b>(3):346–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27095734 27095734]; doi: [https://dx.doi.org/10.1093/cvr/cvw081 10.1093/cvr/cvw081]; GPMDB: [http://gpmdb.org/data/keyword/27095734 12]. | ||
#Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M, (2016) "Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27107777 27107777]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.049 10.1016/j.jprot.2016.03.049]; GPMDB: [http://gpmdb.org/data/keyword/27107777 163]. | #Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M, (2016) "Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27107777 27107777]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.049 10.1016/j.jprot.2016.03.049]; GPMDB: [http://gpmdb.org/data/keyword/27107777 163]. | ||
- | #Larance M, Kirkwood KJ, Tinti M, Murillo | + | #Larance M, Kirkwood KJ, Tinti M, Brenes Murillo A, Ferguson MA, Lamond AI, (2016) "Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(7):2476–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27114452 27114452]; doi: [https://dx.doi.org/10.1074/mcp.O115.055467 10.1074/mcp.O115.055467]; GPMDB: [http://gpmdb.org/data/keyword/27114452 396]. |
#Laghmani K, Beck BB, Yang SS, Seaayfan E, Wenzel A, Reusch B, Vitzthum H, Priem D, Demaretz S, Bergmann K, Duin LK, Göbel H, Mache C, Thiele H, Bartram MP, Dombret C, Altmüller J, Nürnberg P, Benzing T, Levtchenko E, Seyberth HW, Klaus G, Yigit G, Lin SH, Timmer A, de Koning TJ, Scherjon SA, Schlingmann KP, Bertrand MJ, Rinschen MM, de Backer O, Konrad M, Kömhoff M, (2016) "Polyhydramnios, Transient Antenatal Bartter's Syndrome, and MAGED2 Mutations." <i>N Engl J Med</i> <b>374</b>(19):1853–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27120771 27120771]; doi: [https://dx.doi.org/10.1056/NEJMoa1507629 10.1056/NEJMoa1507629]; GPMDB: [http://gpmdb.org/data/keyword/27120771 21]. | #Laghmani K, Beck BB, Yang SS, Seaayfan E, Wenzel A, Reusch B, Vitzthum H, Priem D, Demaretz S, Bergmann K, Duin LK, Göbel H, Mache C, Thiele H, Bartram MP, Dombret C, Altmüller J, Nürnberg P, Benzing T, Levtchenko E, Seyberth HW, Klaus G, Yigit G, Lin SH, Timmer A, de Koning TJ, Scherjon SA, Schlingmann KP, Bertrand MJ, Rinschen MM, de Backer O, Konrad M, Kömhoff M, (2016) "Polyhydramnios, Transient Antenatal Bartter's Syndrome, and MAGED2 Mutations." <i>N Engl J Med</i> <b>374</b>(19):1853–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27120771 27120771]; doi: [https://dx.doi.org/10.1056/NEJMoa1507629 10.1056/NEJMoa1507629]; GPMDB: [http://gpmdb.org/data/keyword/27120771 21]. | ||
- | #Hoehenwarter W, Mönchgesang S, Neumann S, Majovsky P, Abel S, Müller J, (2016) "Comparative expression profiling reveals a role of the root apoplast in local phosphate response." <i>BMC Plant Biol</i> <b>16</b> | + | #Hoehenwarter W, Mönchgesang S, Neumann S, Majovsky P, Abel S, Müller J, (2016) "Comparative expression profiling reveals a role of the root apoplast in local phosphate response." <i>BMC Plant Biol</i> <b>16</b>:106; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27121119 27121119]; doi: [https://dx.doi.org/10.1186/s12870-016-0790-8 10.1186/s12870-016-0790-8]; GPMDB: [http://gpmdb.org/data/keyword/27121119 23]. |
#Eyckerman S, Titeca K, Van Quickelberghe E, Cloots E, Verhee A, Samyn N, De Ceuninck L, Timmerman E, De Sutter D, Lievens S, Van Calenbergh S, Gevaert K, Tavernier J, (2016) "Trapping mammalian protein complexes in viral particles." <i>Nat Commun</i> <b>7</b>:11416; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27122307 27122307]; doi: [https://dx.doi.org/10.1038/ncomms11416 10.1038/ncomms11416]; GPMDB: [http://gpmdb.org/data/keyword/27122307 58]. | #Eyckerman S, Titeca K, Van Quickelberghe E, Cloots E, Verhee A, Samyn N, De Ceuninck L, Timmerman E, De Sutter D, Lievens S, Van Calenbergh S, Gevaert K, Tavernier J, (2016) "Trapping mammalian protein complexes in viral particles." <i>Nat Commun</i> <b>7</b>:11416; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27122307 27122307]; doi: [https://dx.doi.org/10.1038/ncomms11416 10.1038/ncomms11416]; GPMDB: [http://gpmdb.org/data/keyword/27122307 58]. | ||
#Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI, (2016) "Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines." <i>PLoS One</i> <b>11</b>(4):e0154759; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27128805 27128805]; doi: [https://dx.doi.org/10.1371/journal.pone.0154759 10.1371/journal.pone.0154759]; GPMDB: [http://gpmdb.org/data/keyword/27128805 72]. | #Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI, (2016) "Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines." <i>PLoS One</i> <b>11</b>(4):e0154759; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27128805 27128805]; doi: [https://dx.doi.org/10.1371/journal.pone.0154759 10.1371/journal.pone.0154759]; GPMDB: [http://gpmdb.org/data/keyword/27128805 72]. | ||
- | #Petrone A, Adamo ME, | + | #Petrone A, Adamo ME, Cheng C, Kettenbach AN, (2016) "Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics." <i>Mol Cell Proteomics</i> <b>15</b>(7):2448–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27134283 27134283]; doi: [https://dx.doi.org/10.1074/mcp.M116.059394 10.1074/mcp.M116.059394]; GPMDB: [http://gpmdb.org/data/keyword/27134283 90]. |
#Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190]. | #Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190]. | ||
#Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i> <b>8</b>(6):643–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | #Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i> <b>8</b>(6):643–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | ||
- | #Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven | + | #Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven Antigen Discovery for Development of Vaccines Against Gonorrhea." <i>Mol Cell Proteomics</i> <b>15</b>(7):2338–55; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3]. |
#Masuishi Y, Kimura Y, Arakawa N, Hirano H, (2016) "Data for identification of GPI-anchored peptides and ω-sites in cancer cell lines." <i>Data Brief</i> <b>7</b>:1302–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141528 27141528]; doi: [https://dx.doi.org/10.1016/j.dib.2016.04.001 10.1016/j.dib.2016.04.001]; GPMDB: [http://gpmdb.org/data/keyword/27141528 42]. | #Masuishi Y, Kimura Y, Arakawa N, Hirano H, (2016) "Data for identification of GPI-anchored peptides and ω-sites in cancer cell lines." <i>Data Brief</i> <b>7</b>:1302–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141528 27141528]; doi: [https://dx.doi.org/10.1016/j.dib.2016.04.001 10.1016/j.dib.2016.04.001]; GPMDB: [http://gpmdb.org/data/keyword/27141528 42]. | ||
- | #Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA Jr, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM, (2016) "The | + | #Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA Jr, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM, (2016) "The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids." <i>Mol Cell Proteomics</i> <b>15</b>(7):2366–78; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27143409 27143409]; doi: [https://dx.doi.org/10.1074/mcp.M115.056036 10.1074/mcp.M115.056036]; GPMDB: [http://gpmdb.org/data/keyword/27143409 28]. |
#Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. | #Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. | ||
#Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | #Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | ||
- | #Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, | + | #Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, Kumaar LK, Samal A, Rao KV, Kumar D, Nandicoori VK, (2016) "Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns." <i>J Biol Chem</i> <b>291</b>(27):14257–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16]. |
- | #Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ, (2016) "Identification and | + | #Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ, (2016) "Identification and Characterization of Potential Biomarkers by Quantitative Tissue Proteomics of Primary Lung Adenocarcinoma." <i>Mol Cell Proteomics</i> <b>15</b>(7):2396–410; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27161446 27161446]; doi: [https://dx.doi.org/10.1074/mcp.M115.057026 10.1074/mcp.M115.057026]; GPMDB: [http://gpmdb.org/data/keyword/27161446 60]. |
#Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | #Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | ||
- | #Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of | + | #Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of Cellvibrio japonicus during growth on chitin." <i>Proteomics</i> <b>16</b>(13):1904–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18]. |
#Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The clathrin-dependent spindle proteome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130]. | #Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The clathrin-dependent spindle proteome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130]. | ||
#Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA, (2016) "Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex." <i>Cell Rep</i> <b>15</b>(8):1782–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4]. | #Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA, (2016) "Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex." <i>Cell Rep</i> <b>15</b>(8):1782–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4]. | ||
- | #Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma and pseudoexfoliation syndrome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. | + | #Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma, and pseudoexfoliation syndrome." <i>Proteomics</i> <b>16</b>(13):1938–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. |
#Heaven MR, Flint D, Randall SM, Sosunov AA, Wilson L, Barnes S, Goldman JE, Muddiman DC, Brenner M, (2016) "Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease." <i>J Proteome Res</i> <b>15</b>(7):2265–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193225 27193225]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00316 10.1021/acs.jproteome.6b00316]; GPMDB: [http://gpmdb.org/data/keyword/27193225 8]. | #Heaven MR, Flint D, Randall SM, Sosunov AA, Wilson L, Barnes S, Goldman JE, Muddiman DC, Brenner M, (2016) "Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease." <i>J Proteome Res</i> <b>15</b>(7):2265–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193225 27193225]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00316 10.1021/acs.jproteome.6b00316]; GPMDB: [http://gpmdb.org/data/keyword/27193225 8]. | ||
- | #Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27195445 27195445]; doi: [https://dx.doi.org/10.1002/pmic.201500215 10.1002/pmic.201500215]; GPMDB: [http://gpmdb.org/data/keyword/27195445 12]. | + | #Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i> <b>16</b>(13):1872–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27195445 27195445]; doi: [https://dx.doi.org/10.1002/pmic.201500215 10.1002/pmic.201500215]; GPMDB: [http://gpmdb.org/data/keyword/27195445 12]. |
#Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | #Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | ||
#Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of maturation-specific proteins by single-cell proteomics of human oocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18]. | #Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of maturation-specific proteins by single-cell proteomics of human oocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18]. | ||
Line 1,183: | Line 1,183: | ||
#Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | #Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | ||
#Rakus D, Gizak A, Wiśniewski JR, (2016) "Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27302655 27302655]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01149 10.1021/acs.jproteome.5b01149]; GPMDB: [http://gpmdb.org/data/keyword/27302655 60]. | #Rakus D, Gizak A, Wiśniewski JR, (2016) "Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27302655 27302655]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01149 10.1021/acs.jproteome.5b01149]; GPMDB: [http://gpmdb.org/data/keyword/27302655 60]. | ||
- | #Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 | + | #Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 25]. |
#Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. | #Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. | ||
+ | #Ahrné E, Glatter T, Viganò C, Schubert CV, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 24]. | ||
+ | #Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG, (2016) "Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27364158 27364158]; doi: [https://dx.doi.org/10.1074/mcp.M116.060582 10.1074/mcp.M116.060582]; GPMDB: [http://gpmdb.org/data/keyword/27364158 49]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of July 10, 2016.